There is strong evidence that immunological self tolerance critically relies on the elimination of potentially autoaggressive T lymphocyte clones from the emerging immune repertoire during intrathymic T cell differentiation. These 'forbidden' T cells are deleted as a result of a confrontation with their specific self antigen as presented on medullary stroma cells. But this purging mechanism is remarkably leaky, allowing numerous autoreactive T cells to join the healthy immune repertoire. A paper in this issue of the European Journal of Immunology studies the effect of organ-specific autoantigen expression on the cognate T cell repertoire. Myelin oligodendrocyte glycoprotein (MOG), a putative autoantigen in human multiple sclerosis, is used as a model self antigen. T cell receptor profiles in wild-type mice were compared with those in MOG-knock-out mice. Surprisingly, significant differences were not found suggesting that, in this particular case, autoantigen expression does not affect the autoreactive T cell repertoire. Rheumatoid arthritis, type 1 diabetes mellitus and multiple sclerosis (MS) are distinct diseases, but they share one essential common trait i.e. their pathogenesis involves an attack on the body's own organs by autoantigen-specific lymphocytes. In the case of MS, this autoaggressive T cell population is believed to target myelin antigens within the central nervous system (CNS) where their activation triggers an inflammatory cascade that results in tissue edema, demyelination and neuronal damage, the pathology that underlies the severe irreversible neurological deficits that are characteristic of MS.The question of why the immune system in these diseases turns from being beneficial (protective against microbial infections and tumor growth) to pathogenic is one of the core issues in contemporary medicine. We are still seeking answers to a range of fundamental questions that range from the origin of autoaggressive T cells, the mechanisms by which they reach their target tissues and, crucially, how these aberrant pathogenic processes can be controlled therapeutically.